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RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

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  • RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

    http://mammalia.gsc.riken.jp/swine_influenza/

    The new deposits include the first test in Mexico City:
    (this is the site Toaster2 posted about)

    LOCUS GQ292941 558 bp cRNA linear VRL 23-JUN-2009
    DEFINITION Influenza A virus (A/Mexico City/1/2009(H1N1)) segment 4
    hemagglutinin (HA) gene, partial cds.
    ACCESSION GQ292941
    VERSION GQ292941.1 GI:241872078
    DBLINK Project:37813
    KEYWORDS .
    SOURCE Influenza A virus (A/Mexico City/1/2009(H1N1))
    ORGANISM Influenza A virus (A/Mexico City/1/2009(H1N1))
    Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
    Influenzavirus A.
    REFERENCE 1 (bases 1 to 558)
    AUTHORS Zepeda-Lopez,H.M., Perea-Araujo,L.L., Zarate-Segura,P.B.,
    Vazquez-Perez,J.A., Miliar-Garcia,A., Garibay-Orijel,C.,
    Dominguez-Lopez,A., Badillo-Corona,J.A., Garcia-Gonzalez,O.P.,
    Aguilar-Faisan,L. and Bravo-Madrigal,J.
    TITLE Influenza A (H1N1) in Mexico City during critical outbreak
    JOURNAL Unpublished
    REFERENCE 2 (bases 1 to 558)
    AUTHORS Zepeda-Lopez,H.M., Perea-Araujo,L.L., Zarate-Segura,P.B.,
    Vazquez-Perez,J.A., Miliar-Garcia,A., Garibay-Orijel,C.,
    Dominguez-Lopez,A., Badillo-Corona,J.A., Garcia-Gonzalez,O.P.,
    Aguilar-Faisan,L. and Bravo-Madrigal,J.
    TITLE Direct Submission
    JOURNAL Submitted (23-JUN-2009) Laboratorio de Medicina de la Conservacion,
    Escuela Superior de Medicina/Instituto Politecnico Nacional,
    Salvador Diaz Miron esq. Plan de San luis S/N, Mexico City 11340,
    Mexico
    COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
    outbreak of 2009.
    FEATURES Location/Qualifiers
    source 1..558
    /organism="Influenza A virus (A/Mexico City/1/2009(H1N1))"
    /mol_type="viral cRNA"
    /strain="A/Mexico City/1/2009"
    /serotype="H1N1"
    /host="Homo sapiens; age 18 years"
    /db_xref="taxon:654705"
    /segment="4"
    /country="Mexico"
    /collection_date="01-May-2009"
    /note="lineage: swl"
    gene <1..>558
    /gene="HA"
    CDS <1..>558
    /gene="HA"
    /codon_start=1
    /product="hemagglutinin"
    /protein_id="ACS68848.1"
    /db_xref="GI:241872079"
    /translation="HQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQ FTAVGKE
    FNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLY EKVRSQLK
    NNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVK LESTRIYQ
    ILAIYSTVASSLVLVVSLGAISFWMC"
    ORIGIN
    1 catcaaaatg agcaggggtc aggatatgca gccgacctga agagcacaca gaatgccatt
    61 gacgagatta ctaacaaagt aaattctgtt attgaaaaga tgaatacaca gttcacagca
    121 gtaggtaaag agttcaacca cctggaaaaa agaatagaga atttaaataa aaaagttgat
    181 gatggtttcc tggacatttg gacttacaat gccgaactgt tggttctatt ggaaaatgaa
    241 agaactttgg actaccacga ttcaaatgtg aagaacttat atgaaaaggt aagaagccag
    301 ctaaaaaaca atgccaagga aattggaaac ggctgctttg aattttacca caaatgcgat
    361 aacacgtgca tggaaagtgt caaaaatggg acttatgact acccaaaata ctcagaggaa
    421 gcaaaattaa acagagaaga aatagatggg gtaaagctgg aatcaacaag gatttaccag
    481 attttggcga tctattcaac tgtcgccagt tcattggtac tggtagtctc cctgggggca
    541 atcagtttct ggatgtgc

    .
    "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

  • #2
    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

    At least the one above is not yet in the NCBI data base.

    .
    "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

    Comment


    • #3
      Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

      only 3 PB2s are shown and they are all an "E".

      .
      "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

      Comment


      • #4
        Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

        I believe I'm see a "Y" in the NA of GQ293078!

        Influenza A virus (A/Zhejiang/2/2009(H1N1))


        Would someone more knowledgeable please check my work?

        .
        "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

        Comment


        • #5
          Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

          genbank has them on the swine-flu page,
          although some of the records don't load.

          It's not yet available at the search page.


          Does riken allow to download them all into one file ?



          http://mammalia.gsc.riken.jp/swine_influenza/
          I'm interested in expert panflu damage estimates
          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

          Comment


          • #6
            Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

            Originally posted by AlaskaDenise View Post
            I believe I'm see a "Y" in the NA of GQ293078!

            Influenza A virus (A/Zhejiang/2/2009(H1N1))


            Would someone more knowledgeable please check my work?

            .

            I see a H : ...APNYHY...
            position 275
            I'm interested in expert panflu damage estimates
            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

            Comment


            • #7
              Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

              I left out the position I was referencing (obviously), I meant 274.

              Their "[NA of A/Zhejiang/2/2009(H1N1) : GQ293078] Mutation information"
              scroll down window on the lower right clearly reads " 274Y".

              If the mutation line format is confusing, it helps to read the "help" link on the 1st page - upper right top line.

              I await Mamabird's reading.

              .
              "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

              Comment


              • #8
                Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

                Thanks to both of you for examining the sequences and sharing with us what you found. The more eyes, the better.
                The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

                Comment


                • #9
                  Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

                  Originally posted by gsgs View Post
                  genbank has them on the swine-flu page,
                  although some of the records don't load.

                  It's not yet available at the search page.........
                  I have problems on the main NCBI page also. It doesn't appear to know about the same data that the Riken database is clearly extracting from NCBI. I'm assuming they have different permissions.

                  I haven't learned how to use the other databases yet, so can't answer your questions on that.

                  .
                  "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

                  Comment


                  • #10
                    Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

                    it's 275, not 274.
                    274 is counting by another system, presumably N2
                    I'm interested in expert panflu damage estimates
                    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                    Comment


                    • #11
                      Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

                      Dr. Niman just explained that we need to see a YYY in the area, not a YHY.

                      So our tami meds still work (for now).

                      Pheeew.

                      .
                      "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

                      Comment


                      • #12
                        Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

                        Originally posted by AlaskaDenise View Post
                        I have problems on the main NCBI page also. It doesn't appear to know about the same data that the Riken database is clearly extracting from NCBI. I'm assuming they have different permissions.

                        I haven't learned how to use the other databases yet, so can't answer your questions on that.

                        .
                        All sequences at NBCI that can be viewed by the public, are public - no permission required.

                        Comment


                        • #13
                          Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

                          Originally posted by niman View Post
                          All sequences at NBCI that can be viewed by the public, are public - no permission required.
                          So why would a sequence segment in the Riken site not show up in a search through the front-door to the NCBI site?

                          A few days ago, it seemed to be a timing issue, i.e., that Riken had a more current update.

                          .
                          "The next major advancement in the health of American people will be determined by what the individual is willing to do for himself"-- John Knowles, Former President of the Rockefeller Foundation

                          Comment


                          • #14
                            Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

                            see also here:

                            http://www.biohealthbase.org/GSearch...antiViralTable


                            http://www.biohealthbase.org/GSearch...ainDetailTable
                            I'm interested in expert panflu damage estimates
                            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                            Comment


                            • #15
                              Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, &amp; 12 Spain

                              Originally posted by AlaskaDenise View Post
                              Dr. Niman just explained that we need to see a YYY in the area, not a YHY.

                              So our tami meds still work (for now).

                              Pheeew.

                              .
                              Thank you very much Alaska Denise. I really do appreciate the analysis. I don't understand it, and I really like the "bottom line".

                              Comment

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